Table 2.
Ribonucleotides identified by LC–MS/MS analysis of P. aeruginosa PA14 tRNA.
| rN Name | Precursor ion (m/z) | Product ion (m/z) | Fragment (V) | Collision (V) | Retention time (min) | Fold change in ribonucleotide synthesis | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| gidA mutant/Wild type | gidA complemented/Wild type | gidA mutant/gidA complemented | |||||||||
| Mean | SD | Mean | SD | Mean | SD | ||||||
| rC | 244.1 | 112.1 | 380 | 8 | 1.6 | 1.02 | 0.02 | 1 | 0.02 | 1.01 | 0.01 |
| rU | 245.1 | 113.1 | 380 | 4 | 2.6 | 0.98 | 0.02 | 0.98 | 0.01 | 1 | 0.01 |
| Ψ | 245.1 | 125.1 | 380 | 8 | 1.44 | 0.98 | 0.04 | 0.98 | 0.04 | 1 | 0.02 |
| D | 247.1 | 115.1 | 380 | 8 | 1.41 | 1.04 | 0.05 | 1.05 | 0.05 | 0.99 | 0.03 |
| Cm | 258.1 | 112.1 | 380 | 8 | 5.1 | 1.17 | 0.09 | 1.18 | 0.07 | 0.99 | 0.06 |
| m5C | 258.1 | 126.1 | 380 | 8 | 2.7 | 0.96 | 0.31 | 1.3 | 0.41 | 0.74 | 0.05 |
| m3C | 258.1 | 126.1 | 380 | 8 | 2.2 | 0.81 | 0.57 | 0.94 | 0.61 | 0.81 | 0.18 |
| Um | 259.1 | 113.1 | 380 | 4 | 9.1 | 3.06 | 1.63 | 3.06 | 1.5 | 1 | 0.15 |
| m5U | 259.1 | 127.1 | 380 | 8 | 6.3 | 0.94 | 0.05 | 0.95 | 0.07 | 0.99 | 0.04 |
| S4U | 261.1 | 129.1 | 380 | 8 | 7.9 | 0.92 | 0.13 | 0.97 | 0.17 | 0.96 | 0.08 |
| S2U | 261.1 | 129.1 | 380 | 8 | 6.3 | 3.97* | 0.26 | 0.91 | 0.04 | 4.37* | 0.11 |
| rA | 268.1 | 136.1 | 380 | 16 | 5.5 | 1 | 0 | 1 | 0 | 1 | 0 |
| I | 269.1 | 137.1 | 380 | 12 | 6.2 | 0.84 | 0.03 | 0.87 | 0.06 | 0.96 | 0.04 |
| mo5U | 275.1 | 143.1 | 380 | 4 | 7.3 | 0.79 | 0.19 | 0.88 | 0.28 | 0.93 | 0.16 |
| m6A | 282.1 | 150.1 | 380 | 16 | 16.2 | 0.93 | 0.04 | 0.87 | 0.03 | 1.06 | 0.08 |
| m2A | 282.1 | 150.1 | 380 | 16 | 11.5 | 0.96 | 0.06 | 0.95 | 0.08 | 1.01 | 0.02 |
| Am | 282.1 | 136.1 | 380 | 16 | 12.4 | 1.07 | 0.42 | 1.03 | 0.37 | 1.11 | 0.42 |
| rG | 284.1 | 152.1 | 380 | 16 | 6.9 | 1 | 0.01 | 1 | 0.01 | 1 | 0.01 |
| mnm5U | 288.1 | 125 | 380 | 20 | 1.6 | 0.06* | 0.01 | 1.15 | 0.19 | 0.05* | 0 |
| m62A | 296.1 | 164.1 | 380 | 16 | 20.4 | 0.5 | 0.25 | 1.12 | 0.41 | 0.44* | 0.07 |
| Gm | 298.1 | 152.1 | 380 | 8 | 15 | 0.99 | 0.2 | 0.94 | 0.23 | 1.06 | 0.05 |
| m7G | 298.1 | 166.1 | 380 | 12 | 5.1 | 0.91 | 0.02 | 0.95 | 0.02 | 0.96 | 0.03 |
| m1G | 298.1 | 166.1 | 380 | 12 | 15 | 0.99 | 0.24 | 0.9 | 0.16 | 1.11 | 0.26 |
| m22G | 312.1 | 180.1 | 380 | 8 | 19.5 | 0.47 | 0.4 | 0.75 | 0.53 | 0.57 | 0.13 |
| cmo5U | 319 | 187 | 380 | 8 | 6.5 | 0.78 | 0.09 | 0.86 | 0.08 | 0.91 | 0.03 |
| cmnm5U | 332.1 | 125 | 380 | 18 | 1.6 | 0.18* | 0.03 | 0.93 | 0.11 | 0.19* | 0.02 |
| i6A | 336.2 | 204.2 | 380 | 16 | 22.4 | 0.74 | 0.23 | 0.67 | 0.19 | 1.1 | 0.19 |
| cmnm5s2U | 348.1 | 141.1 | 380 | 20 | 3.7 | 0.53 | 0.75 | 1.11 | 0.73 | 0.35 | 0.33 |
| t6A | 413.1 | 281.1 | 380 | 8 | 21.9 | 0.91 | 0.04 | 0.92 | 0.03 | 0.99 | 0.02 |
Asterisks denote a significant difference in the one-way ANOVA (*p ≤ 0.05).